4B9M Transferase Dna date Sep 05, 2012
title Structure Of The High Fidelity Dna Polymerase I With An Oxidative Formamidopyrimidine-Da Dna Lesion -Thymine Basepair In The Post-Insertion Site.
authors T.H.Gehrke, U.Lischke, S.Arnold, S.Schneider, T.Carell
compound source
Molecule: Dna Polymerase I
Chain: A
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Pdest007
Other_details: German Collection Of Microorganisms Dsm No.

Molecule: 5'-D(Gpcpcptpgpapcptpcptptp)-3'
Chain: B

Synthetic: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422

Molecule: 5'-D(Dcdadafaxapgpapgptpcpapgpgpcp
Chain: C

Synthetic: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
symmetry Space Group: P 21 21 21
R_factor 0.18574 R_Free 0.22098
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.419 93.656 105.053 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand FAX, MG, SO4 enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • 3'-5' exonuclease activity


  • Primary referenceUnexpected non-Hoogsteen-based mutagenicity mechanism of FaPy-DNA lesions., Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T, Nat Chem Biol. 2013 May 19. doi: 10.1038/nchembio.1254. PMID:23685671
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (228 Kb) [Save to disk]
  • Biological Unit Coordinates (4b9m.pdb1.gz) 220 Kb
  • LPC: Ligand-Protein Contacts for 4B9M
  • CSU: Contacts of Structural Units for 4B9M
  • Structure Factors (366 Kb)
  • Retrieve 4B9M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4B9M from S2C, [Save to disk]
  • Re-refined 4b9m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
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  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4B9M, from MSDmotif at EBI
  • Fold representative 4b9m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4b9m_C] [4b9m_A] [4b9m] [4b9m_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4B9M: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 4B9M
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